git:20260915.b09a383 to git:20260930.913abeb

- You are helping a medical researcher draft a research protocol for IRB/ethics committee

- submission. This skill generates the scientific core of the protocol while providing

- structured skeletons for institution-specific sections.

-

- ## Scope

-

- This skill generates **4 core sections** with full prose:

- 1. Background and Rationale

- 2. Study Design and Eligibility Criteria

- 3. Sample Size Justification

- 4. Statistical Analysis Plan

-

- The remaining **6 sections** are provided as structured skeletons with `[TODO]` markers,

- because they vary significantly across institutions, countries, and regulatory frameworks.

-

- **Important**: This protocol is a STARTING POINT. Every institution has its own IRB

- submission form and requirements. The generated protocol must be adapted to your

- institution's specific format before submission.

-

- ## Reference Files

-

- - **Protocol template**: `${CLAUDE_SKILL_DIR}/references/protocol_template.md` -- complete 10-section structure with formatting guidance

- - **Ethics checklist**: `${CLAUDE_SKILL_DIR}/references/ethics_checklist.md` -- jurisdiction-specific ethical requirements

-

- Read both reference files before generating a protocol draft.

-

- ## Cross-Skill Integration

-

- - **Input from design-study**: Study design recommendations, analysis unit, comparator design, validation strategy

- - **Input from calc-sample-size**: `protocol/sample_size_justification.md` (canonical IRB-ready prose) + `protocol/sample_size_calc.{R,py}` (reproducible code). Embed `sample_size_justification.md` VERBATIM into Methods §Sample Size — do not rephrase numbers (per `~/.claude/rules/numerical-safety.md`).

- - **Input from search-lit**: Background references with verified citations

- - **Input from define-variables**: `variable_operationalization.md` — literature-grounded definitions, cutoffs, DB-variable mappings for the Methods section. **Precondition**: if the study is observational and no operationalization artifact exists, call `/define-variables` before drafting Methods. Do not invent phenotype/cutoff definitions from the data dictionary inside this skill.

- - **Pipeline position**: search-lit -> design-study -> calc-sample-size -> define-variables -> **write-protocol** -> manage-project

-

- When prior skill outputs are available, incorporate them directly. When they are not,

- prompt the user or call the relevant skill.

-

- ---

-

- ## Communication Rules

-

- - Communicate with the user in their preferred language.

- - Use English for all protocol content, statistical terminology, and medical terminology.

- - Be explicit about what is generated versus what requires institutional input.

- ---

- ## Required Inputs

- Collect all required inputs before generating. Ask one question at a time if information is missing.

- 1. **Research question / hypothesis** -- specific, testable

- 2. **Study type** -- retrospective cohort, prospective cohort, cross-sectional, RCT, diagnostic accuracy, case-control, case series

- 3. **Target population** -- who, where, when

- 4. **Primary outcome** -- what you are measuring

- 5. **Secondary outcomes** (if any)

- ## Optional Inputs (enhance quality if available)

- 6. **design-study output** -- if `/design-study` was already run, load its recommendations

- 7. **calc-sample-size output** -- if `/calc-sample-size` was already run, load its results and IRB text

- 8. **Key references** -- DOIs or search terms for background section

- 9. **Institution name** -- for header and ethics section guidance

- 10. **Regulatory context** -- Korea (PIPA), US (HIPAA/Common Rule), EU (GDPR), other

- Generate full prose covering:

- - **Clinical context**: disease burden, current practice, knowledge gap

- - **Literature support**: call `/search-lit` if key references are not provided; every citation must have a verified DOI or PMID

- - **Rationale**: why this study is needed, what it adds to existing evidence

- - **Research question**: clear statement of the hypothesis or research question

-

- Do not use bullet points in the output. Write in full paragraphs with logical flow from

- clinical context through knowledge gap to research question.

- Generate full prose plus structured criteria lists:

- - **Study design** with justification (why this design answers this question)

- - **Setting**: single-center vs multi-center, institution description

- - **Study period**: start and end dates or planned duration

- - **Inclusion criteria** (numbered list)

- - **Exclusion criteria** (numbered list)

-

- If design-study output is available, incorporate its recommendations on:

- - Analysis unit (patient vs lesion vs exam)

- - Comparator design

- - Validation strategy

- - Potential leakage risks and mitigations

- - If `protocol/sample_size_justification.md` exists (calc-sample-size output): embed VERBATIM. Do not rephrase numbers.

- - If not available: prompt the user to run `/calc-sample-size` first; only fall back to a basic justification if the user explicitly declines.

- - Must include: test type, expected effect size (with literature source), alpha level, power, attrition adjustment

- Generate full prose covering:

- - **Descriptive statistics**: continuous variables as mean (SD) or median (IQR); categorical variables as count (%)

- - **Primary analysis**: statistical test, assumptions, handling of violations

- - **Secondary analyses**: pre-specified

- - **Subgroup analyses**: pre-specified, with interaction tests

- - **Missing data**: handling strategy (complete case, multiple imputation, sensitivity analysis)

- - **Software**: name and version (e.g., R 4.4.0, Python 3.12, SAS 9.4)

- - **Significance level**: two-sided alpha = 0.05 unless otherwise justified

- #### Section 5: Study Title and Registration

-

- ```

- [TODO: Full study title]

- [TODO: Short title / acronym]

- [TODO: Clinical trial registry number if applicable (e.g., ClinicalTrials.gov, CRIS)]

- [TODO: Protocol version number and date]

- ```

-

- #### Section 6: Data Collection and Management

-

- ```

- [TODO: List variables to be collected -- use your institution's case report form (CRF) template]

- [TODO: Data collection method (chart review / prospective forms / electronic extraction)]

- [TODO: Data storage and security measures (encrypted database, access controls)]

- [TODO: Quality assurance procedures (double data entry, range checks)]

- [TODO: Data retention period per institutional policy]

- ```

-

- #### Section 7: Ethical Considerations

-

- ```

- [TODO: IRB/Ethics committee name and expected submission date]

- [TODO: Informed consent process -- or justification for waiver]

- [TODO: Patient privacy and data protection measures]

- ```

-

- Include regulatory guidance by jurisdiction:

- - **Korea**: Personal Information Protection Act (PIPA), Bioethics and Safety Act

- - **United States**: HIPAA Privacy Rule, Common Rule (45 CFR 46)

- - **European Union**: GDPR Article 9 (health data), Clinical Trials Regulation (EU 536/2014)

-

- ```

- [TODO: Confirm applicable regulations with your IRB office]

- ```

-

- Refer to `${CLAUDE_SKILL_DIR}/references/ethics_checklist.md` for the full checklist.

-

- #### Section 8: Timeline and Milestones

-

- ```

- [TODO: Adapt to your project schedule]

-

- | Phase | Activity | Duration | Target Date |

- |-------|---------------------------------------|-------------|-------------|

- | 1 | IRB approval | [X] weeks | [TODO] |

- | 2 | Data collection / Patient enrollment | [X] months | [TODO] |

- | 3 | Data cleaning and analysis | [X] months | [TODO] |

- | 4 | Manuscript preparation | [X] months | [TODO] |

- | 5 | Submission | -- | [TODO] |

- ```

-

- #### Section 9: Budget

- ```

- [TODO: Use your institution's budget template]

- [TODO: Common cost categories below -- delete or add as needed]

- - Personnel (research coordinator, statistician)

- - Equipment and supplies

- - Software licenses

- - Statistical consultation

- - Publication fees (open access APC)

- - Patient compensation (if applicable)

- ```

- Generate a numbered reference list from:

- - Citations used in Section 1 (Background and Rationale)

- - Effect size sources from Section 3 (Sample Size Justification)

- - Any additional references from calc-sample-size output

-

- All references must have verified DOIs or PMIDs. Mark any unverified references

- as `[UNVERIFIED - NEEDS MANUAL CHECK]`.

- Requirements:

- - Core sections (1-4) in full prose, no bullet points in body text

- After generating, inform the user:

- 1. Which sections are complete and ready for review

- 2. Which `[TODO]` items require their input

- 3. Recommended next steps (e.g., "Fill in Section 5 title and registration, then adapt Section 7 to your IRB form")

-

- ---

- 1. **Citation integrity**: Every reference has a DOI or PMID, or is marked `[UNVERIFIED]`

- 2. **Internal consistency**: Sample size in Section 3 matches the analysis plan in Section 4

- 3. **Design alignment**: Study type in Section 2 matches the statistical approach in Section 4

- 4. **TODO completeness**: All institution-specific items have `[TODO]` markers

- 5. **Word counts**: Core sections fall within target ranges

- 6. **No AI patterns**: Avoid phrases like "it is worth noting", "comprehensive", "plays a crucial role"

-

- ## Anti-Hallucination

-

- - **Never fabricate references.** All citations must be verified via `/search-lit` with confirmed DOI or PMID. Mark unverified references as `[UNVERIFIED - NEEDS MANUAL CHECK]`.

- - **Never invent clinical definitions, diagnostic criteria, or guideline recommendations.** If uncertain, flag with `[VERIFY]` and ask the user.

-

- ## Global-rule references

-

- Some passages in this skill cite a path of the form `~/.claude/rules/<name>.md`. Those are the

- maintainer's personal global rules, kept outside this repository. They are **not shipped with

- this skill** and will not exist on your machine; they appear only as provenance for where a

- convention came from. If one of them looks like it is standing in for an instruction you actually

- need, that is a bug — please open an issue, because the instruction belongs here.